Résumé
Species inventories are the building blocks of our assessment of
biodiversity patterns and human impact. Yet, historical inventories based
on visual observations are often incomplete impairing subsequent analyses
of ecological mechanisms, extinction risk and management success.
Environmental DNA (eDNA) metabarcoding is an emerging tool that can
provide wider biodiversity assessments than classical visual-based
surveys. However, eDNA-based inventories remain limited by sampling effort
and reference database incompleteness. In this study, we propose a new
framework coupling eDNA surveys and sampling-theory methods to estimate
species richness in under-sampled and hyper-diverse regions where some
species remain absent from the checklist or undetected by visual surveys.
We applied this framework to the coastal fish diversity in the heart of
the Coral Triangle, the richest marine biodiversity hotspot worldwide.
Combining data from 279 underwater visual censuses, 92 eDNA samples and an
extensive custom genetic reference database, we show that eDNA
metabarcoding recorded 196 putative species not detected by underwater
visual census including 37 species absent from the regional checklist. We
provide an updated checklist of marine fishes in the 'Raja Ampat
Bird's Head Peninsula' ecoregion with 2,534 species including
1,761 confirmed and 773 highly probable presences. The Chao lower-bound
diversity estimator, based on the incidence of rare species, shows that
the region potentially hosts an additional 123 fish species, including
pelagic, cryptobenthic and vulnerable species. The extended and hidden
biodiversity along with their asymptotic estimates highlight the ability
of eDNA to expand regional inventories and species distributions to better
guide conservation strategies.